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2py5

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(New page: 200px<br /><applet load="2py5" size="450" color="white" frame="true" align="right" spinBox="true" caption="2py5, resolution 1.60&Aring;" /> '''Phi29 DNA polymerase...)
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[[Image:2py5.jpg|left|200px]]<br /><applet load="2py5" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2py5, resolution 1.60&Aring;" />
 
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'''Phi29 DNA polymerase complexed with single-stranded DNA'''<br />
 
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==Overview==
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==Phi29 DNA polymerase complexed with single-stranded DNA==
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Replicative DNA polymerases (DNAPs) move along template DNA in a, processive manner. The structural basis of the mechanism of translocation, has been better studied in the A-family of polymerases than in the, B-family of replicative polymerases. To address this issue, we have, determined the X-ray crystal structures of phi29 DNAP, a member of the, protein-primed subgroup of the B-family of polymerases, complexed with, primer-template DNA in the presence or absence of the incoming nucleoside, triphosphate, the pre- and post-translocated states, respectively., Comparison of these structures reveals a mechanism of translocation that, appears to be facilitated by the coordinated movement of two conserved, tyrosine residues into the insertion site. This differs from the mechanism, employed by the A-family polymerases, in which a conserved tyrosine moves, into the templating and insertion sites during the translocation step., Polymerases from the two families also interact with downstream, single-stranded template DNA in very different ways.
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<StructureSection load='2py5' size='340' side='right'caption='[[2py5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2py5]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY5 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2py5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py5 OCA], [https://pdbe.org/2py5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py5 RCSB], [https://www.ebi.ac.uk/pdbsum/2py5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2py5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2py5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.
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==About this Structure==
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Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.,Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604<ref>PMID:17611604</ref>
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2PY5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with EDO as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PY5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases., Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA, EMBO J. 2007 Jul 5;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17611604 17611604]
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 2py5" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Vibrio phage f237]]
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[[Category: Berman, A.J.]]
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[[Category: Blanco, L.]]
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[[Category: Goodman, J.L.]]
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[[Category: Kamtekar, S.]]
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[[Category: Lazaro, J.M.]]
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[[Category: Salas, M.]]
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[[Category: Steitz, T.A.]]
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[[Category: Vega, M.de.]]
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[[Category: EDO]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:44:01 2007''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus virus phi29]]
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[[Category: Large Structures]]
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[[Category: Berman AJ]]
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[[Category: Blanco L]]
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[[Category: Goodman JL]]
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[[Category: Kamtekar S]]
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[[Category: Lazaro JM]]
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[[Category: Salas M]]
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[[Category: Steitz TA]]
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[[Category: De Vega M]]

Current revision

Phi29 DNA polymerase complexed with single-stranded DNA

PDB ID 2py5

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